Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street S.E. Minneapolis, MN 55455, USA.
Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, 60439, USA.
Nucleic Acids Res. 2018 Nov 2;46(19):10474-10488. doi: 10.1093/nar/gky776.
DNA ligases play essential roles in DNA replication and repair. Bacteriophage T4 DNA ligase is the first ATP-dependent ligase enzyme to be discovered and is widely used in molecular biology, but its structure remained unknown. Our crystal structure of T4 DNA ligase bound to DNA shows a compact α-helical DNA-binding domain (DBD), nucleotidyl-transferase (NTase) domain, and OB-fold domain, which together fully encircle DNA. The DBD of T4 DNA ligase exhibits remarkable structural homology to the core DNA-binding helices of the larger DBDs from eukaryotic and archaeal DNA ligases, but it lacks additional structural components required for protein interactions. T4 DNA ligase instead has a flexible loop insertion within the NTase domain, which binds tightly to the T4 sliding clamp gp45 in a novel α-helical PIP-box conformation. Thus, T4 DNA ligase represents a prototype of the larger eukaryotic and archaeal DNA ligases, with a uniquely evolved mode of protein interaction that may be important for efficient DNA replication.
DNA 连接酶在 DNA 复制和修复中发挥着重要作用。噬菌体 T4 DNA 连接酶是第一个被发现的依赖于 ATP 的连接酶，广泛应用于分子生物学，但它的结构仍然未知。我们解析的与 DNA 结合的 T4 DNA 连接酶的晶体结构显示出一个紧凑的 α-螺旋 DNA 结合域（DBD）、核苷酸转移酶（NTase）结构域和 OB 折叠结构域，它们共同完全环绕 DNA。T4 DNA 连接酶的 DBD 与真核生物和古菌 DNA 连接酶较大的 DBD 的核心 DNA 结合螺旋具有显著的结构同源性，但它缺乏用于蛋白质相互作用的其他结构成分。相反，T4 DNA 连接酶在 NTase 结构域内有一个灵活的环插入，以新颖的 α-螺旋 PIP 盒构象与 T4 滑动夹 gp45 紧密结合。因此，T4 DNA 连接酶代表了较大的真核生物和古菌 DNA 连接酶的原型，具有独特进化的蛋白质相互作用模式，这可能对高效的 DNA 复制很重要。
